Scientific
MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis
These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.
MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.
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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX
Showing element 633 to 682 of 3228 in total
Value Type: Ranked
Network Comparison Type: Divided
Interaction Map: High confidence
Filtered: 1

\def\wcA{0.16666666666667\textwidth}
\def\wcB{0.16666666666667\textwidth}
\def\wcC{0.16666666666667\textwidth}
\def\wcD{0.16666666666667\textwidth}
\def\wcE{0.16666666666667\textwidth}
\begin{longtable}{|c|c|c|c|c|}
\hline
\parbox{\wcA}{\vspace{3pt}\noindent
Rank\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
description\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
red\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
green\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
network\_comparison\vspace{3pt}}\\
\hline
\hline
\parbox{\wcA}{\vspace{3pt}\noindent
633\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [source:swissprot;acc:p49588]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
234.106\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
248.104\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
1.05979\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
634\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
dead-box protein abstrakt homolog. [source:swissprot;acc:q9ujv9]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
226.523\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
213.786\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
1.05958\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
635\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
60s ribosomal protein l37 (g1.16). [source:swissprot;acc:p02403]\vspace{3pt}}&\multirow{4}{*}{\parbox{\wcC}{\vspace{3pt}\noindent
228.639\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcD}{\vspace{3pt}\noindent
242.258\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcE}{\vspace{3pt}\noindent
1.05957\vspace{3pt}}}\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
636\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [source:swissprot;acc:q07955]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
637\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [source:swissprot;acc:q06203]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
638\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
sorting nexin 17. [source:swissprot;acc:q15036]\vspace{3pt}}&&&\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
639\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [source:swissprot;acc:p52594]\vspace{3pt}}&\multirow{7}{*}{\parbox{\wcC}{\vspace{3pt}\noindent
217.67\vspace{3pt}}}&\multirow{7}{*}{\parbox{\wcD}{\vspace{3pt}\noindent
230.596\vspace{3pt}}}&\multirow{7}{*}{\parbox{\wcE}{\vspace{3pt}\noindent
1.05938\vspace{3pt}}}\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
640\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [source:swissprot;acc:q15811]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
641\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [source:refseq;acc:nm\_032152]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
642\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [source:swissprot;acc:q9nzm3]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
643\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [source:refseq;acc:nm\_006076]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
644\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
cgthba protein (-14 gene protein). [source:swissprot;acc:q12980]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
645\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [source:refseq;acc:nm\_014500]\vspace{3pt}}&&&\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
646\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
short coiled-coil protein; short coiled coil protein. [source:refseq;acc:nm\_032547]\vspace{3pt}}&\multirow{2}{*}{\parbox{\wcC}{\vspace{3pt}\noindent
216.731\vspace{3pt}}}&\multirow{2}{*}{\parbox{\wcD}{\vspace{3pt}\noindent
229.549\vspace{3pt}}}&\multirow{2}{*}{\parbox{\wcE}{\vspace{3pt}\noindent
1.05914\vspace{3pt}}}\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
647\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
dynein light chain 2. [source:refseq;acc:nm\_080677]\vspace{3pt}}&&&\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
648\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [source:swissprot;acc:p56192]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
218.227\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
206.078\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
1.05895\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
649\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [source:swissprot;acc:p06730]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
233.725\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
220.751\vspace{3pt}}&\multirow{3}{*}{\parbox{\wcE}{\vspace{3pt}\noindent
1.05877\vspace{3pt}}}\\\cline{1-4}
\parbox{\wcA}{\vspace{3pt}\noindent
650\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
u6 snrna-associated sm-like protein lsm7. [source:swissprot;acc:q9uk45]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
228.986\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
216.276\vspace{3pt}}&\\\cline{1-4}
\parbox{\wcA}{\vspace{3pt}\noindent
651\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
bai1-associated protein 3; bai-associated protein 3. [source:refseq;acc:nm\_003933]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
233.725\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
220.751\vspace{3pt}}&\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
652\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [source:refseq;acc:nm\_014886]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
248.994\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
235.255\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
1.0584\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
653\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
dok-like protein. [source:refseq;acc:nm\_024872]\vspace{3pt}}&\multirow{4}{*}{\parbox{\wcC}{\vspace{3pt}\noindent
216.504\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcD}{\vspace{3pt}\noindent
204.622\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcE}{\vspace{3pt}\noindent
1.05807\vspace{3pt}}}\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
654\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [source:swissprot;acc:o60496]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
655\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [source:swissprot;acc:q99704]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
656\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [source:swissprot;acc:p42685]\vspace{3pt}}&&&\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
657\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
synapsin iii. [source:swissprot;acc:o14994]\vspace{3pt}}&\multirow{13}{*}{\parbox{\wcC}{\vspace{3pt}\noindent
229.072\vspace{3pt}}}&\multirow{13}{*}{\parbox{\wcD}{\vspace{3pt}\noindent
216.576\vspace{3pt}}}&\multirow{13}{*}{\parbox{\wcE}{\vspace{3pt}\noindent
1.0577\vspace{3pt}}}\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
658\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [source:refseq;acc:nm\_032468]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
659\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [source:swissprot;acc:q9y5j3]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
660\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
actin binding lim protein 2. [source:refseq;acc:nm\_032432]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
661\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
hairy/enhancer-of-split related with yrpw motif-like. [source:refseq;acc:nm\_014571]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
662\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
synapsin ii. [source:swissprot;acc:q92777]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
663\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
mitochondrial ribosome recycling factor. [source:refseq;acc:nm\_138777]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
664\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [source:swissprot;acc:p50542]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
665\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [source:refseq;acc:nm\_012259]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
666\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [source:swissprot;acc:q14469]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
667\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [source:swissprot;acc:q13011]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
668\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [source:refseq;acc:nm\_002313]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
669\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
synapsin i (brain protein 4.1). [source:swissprot;acc:p17600]\vspace{3pt}}&&&\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
670\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
autoantigen ngp-1. [source:swissprot;acc:q13823]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
250.302\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
236.817\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
1.05694\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
671\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
nucleotide-binding protein 1 (nbp 1). [source:swissprot;acc:p53384]\vspace{3pt}}&\multirow{2}{*}{\parbox{\wcC}{\vspace{3pt}\noindent
210.739\vspace{3pt}}}&\multirow{2}{*}{\parbox{\wcD}{\vspace{3pt}\noindent
199.398\vspace{3pt}}}&\multirow{2}{*}{\parbox{\wcE}{\vspace{3pt}\noindent
1.05688\vspace{3pt}}}\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
672\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
nucleotide binding protein 2 (nbp 2). [source:swissprot;acc:q9y5y2]\vspace{3pt}}&&&\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
673\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [source:swissprot;acc:o14936]\vspace{3pt}}&\multirow{3}{*}{\parbox{\wcC}{\vspace{3pt}\noindent
226.497\vspace{3pt}}}&\multirow{3}{*}{\parbox{\wcD}{\vspace{3pt}\noindent
214.355\vspace{3pt}}}&\multirow{3}{*}{\parbox{\wcE}{\vspace{3pt}\noindent
1.05664\vspace{3pt}}}\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
674\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [source:refseq;acc:nm\_152794]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
675\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
single-minded homolog 1. [source:swissprot;acc:p81133]\vspace{3pt}}&&&\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
676\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [source:swissprot;acc:p52433]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
232.469\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
245.613\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
1.05654\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
677\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [source:swissprot;acc:q9y4z0]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
228.944\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
216.745\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
1.05628\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
678\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
sorting nexin 5. [source:swissprot;acc:q9y5x3]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
208.482\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
220.175\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
1.05609\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
679\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]\vspace{3pt}}&\multirow{4}{*}{\parbox{\wcC}{\vspace{3pt}\noindent
132.413\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcD}{\vspace{3pt}\noindent
125.389\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcE}{\vspace{3pt}\noindent
1.05602\vspace{3pt}}}\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
680\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
homeobox protein hox-b4 (hox-2f) (hox-2.6). [source:swissprot;acc:p17483]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
681\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
homeobox protein hox-c5 (hox-3d) (cp11). [source:swissprot;acc:q00444]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
682\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]\vspace{3pt}}&&&\\\hline
nd{longtable}

Legend:
- Rank is the rank after comparing the two networks

 - Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray

 - Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.

 - Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them

 - Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.

 - Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/